docs: def run_repair_pdb(self, silent=False, force_rerun=False):
          """Run FoldX RepairPDB on this PDB file.
  
          Original command::
  
              foldx --command=RepairPDB --pdb=4bxi.pdb
  
          Args:
              silent (bool): If FoldX output should be silenced from printing to the shell.
              force_rerun (bool): If FoldX RepairPDB should be rerun even if a repaired file exists.
  
          """
          # Create RepairPDB command
          foldx_repair_pdb = 'foldx --command=RepairPDB --pdb={}'.format(self.pdb_file)
  
          # Repaired PDB output file name
          foldx_repair_outfile = '{}_Repair.pdb'.format(op.splitext(self.pdb_file)[0])
  
          # Run RepairPDB
          ssbio.utils.command_runner(shell_command=foldx_repair_pdb, force_rerun_flag=force_rerun, silent=silent,
                                     outfile_checker=foldx_repair_outfile, cwd=self.foldx_dir)
  
          # TODO: write stdout/stderr to log file somewhere!
  
          self.repaired_pdb_outfile = foldx_repair_outfile